Science Advances

Vaccination programs worldwide have effectively reduced the burden of childhood diseases, yet immune responses remain highly heterogeneous among individuals. While host characteristics such as age and sex are established determinants of vaccine immunogenicity, the timing of vaccination, specifically the calendar season of vaccination, remains largely underexplored. Although circadian rhythms are known to regulate daily immune function, evidence for long-term circannual patterns has been limited by the difficulty of collecting year-round vaccination data across diverse populations. Here, we show that the season of vaccination systematically shapes the immune response across a broad range of pediatric vaccines. By leveraging data from 96 randomized control trials worldwide, including over 48,000 children vaccinated against 14 pathogens, we demonstrate that immunogenicity after vaccination follows a pronounced latitudinal gradient, typically peaking during colder months in temperate regions and exhibiting distinct variability in the tropics. These findings suggest that the circadian human immune response might extend to a circannual scale, potentially synchronized by environmental cues. Incorporating the season of vaccination into the design of clinical trials and public health campaigns may optimize vaccine performance and enhance seroprotection.

To elucidate the contribution of chromatin modifications in plant cold response, we performed ChIP-seq for H3K27me3 and H2A.Z in Arabidopsis exposed to short-term cold. We combined our epigenetic data with NET-seq to investigate the direct transcriptional effects of histone marks. Prior to any stress cue, cold regulated genes share a similar chromatin environment with high H2A.Z and H3K27me3. H3K27me3 levels do not correlate with transcriptional activity or elongation speed. However, REF6-mediated reduction of H3K27me3 is essential for regulation of cold controlled genes. H2A.Z occupancy changes revealed a negative correlation between cold-induced changes to H2A.Z and RNAPII activity at differentially expressed genes. Importantly, changing H2A.Z levels preceded transcriptional changes, indicating that the variant functions as a critical cold-induced switch. Further, our data suggests that high H2A.Z levels slow down RNAPII. Thus, H2A.Z is essential for the transcriptional response and a decreased H3K27me3 level is important for the genomic adaptation to cold.

Midbrain dopamine (DA) neurons critically regulate basal ganglia function through their widespread projections. While the nigrostriatal pathway is well characterized and represents the dominant source of DA in the basal ganglia, other nuclei such as the external Globus Pallidus (GPe) also receive dopaminergic innervation, yet no consensus exists about its precise anatomical origin. In addition, the GABAergic tail of the ventral tegmental area (tVTA) provides a major inhibitory input to midbrain DA neurons, but its influence over DA pathways to the GPe remains unknown. In the rat, we combined retrograde tracing, immunohistochemistry, and ex vivo electrophysiology to identify distinct populations of DA neurons in the substantia nigra pars compacta (SNc) and ventral tegmental area (VTA) that project to the GPe and display distinct electrophysiological properties. Using optogenetics and electrophysiology, we also demonstrate that these GPe-projecting DA neurons receive powerful inhibitory input from the tVTA. Together, our findings define both the origin and inhibitory control of dopaminergic innervation to the GPe, revealing a previously unrecognized disynaptic circuit (tVTA[->]DA[->]GPe) that refines our understanding of basal ganglia circuit function.

Endosymbiosis of phytoplankton in heterotrophic hosts is ecologically important and has led to key evolutionary innovations. However, the dynamic molecular processes underlying endosymbiosis establishment remain poorly understood. Here, using large-particle sorting and liquid chromatography-tandem mass spectrometry, we unravel heterogeneous changes in proteomes of the cosmopolitan ciliate Paramecium and algal endosymbiont Chlorella from engulfment to stable endosymbiosis. The initial digestion sees a sharp decline of intracellular Chlorella cells, along with host cellular reorganization involving a reduction of the cortex-localized defensive organelles, trichocysts, and proteins for intracellular transport and recycling. The remaining Chlorella cells enter a bottleneck stage characterized by energy production and cell cycle commitment before active proliferation. Comparison of Paramecium with successful and failed endosymbiosis further identifies a solute carrier transporter that potentially mediates metabolic homeostasis of the endosymbiotic system. Our study reveals inter-organismal coordination during the transition from predator-prey to host-endosymbiont relationships. The approach of time-course single-cell dual proteomics can be useful for investigating diverse interactions between microbial eukaryotes.

Visual surface perception is a fundamental aspect of vision, yet its neural implementation remains poorly understood. Troxlers perceptual filling-in paradigm provides a tractable illusion for studying surface perception, in which a peripheral figure becomes perceptually assimilated into the surrounding background after a period of sustained fixation. Although neural correlates of this phenomenon have been reported in early visual cortex, the underlying mechanisms, particularly the contribution of feedback signaling, remain unresolved. Here we use ultra-high-field (7T) layer-fMRI to investigate perceptual filling-in in the human visual cortex. While experimentally controlling perceptual filling-in, we measured GE-BOLD responses in ten participants. Analyses across cortical depth in the independently localized figure representation in primary visual cortex (V1) revealed neural correlates of filling-in in deep cortical layers, which are associated with feedback input. These findings provide evidence that perceptual filling-in and visual surface perception in general are supported by feedback signals to early visual cortex.

Persistent detection of high-risk human papillomavirus (HPV) is required for cervical carcinogenesis, yet the metabolic phenotype associated with distinct HPV transition states remains incompletely defined. We analyzed vaginal metabolomics data from 71 HIV-negative, non-smoking, premenopausal women without other sexually transmitted infections, grouped by three-visit HPV trajectories: persistent negative (NNN, n=20), late incident positivity (NNP, n=9), conversion with persistence (NPP, n=13), clearance after prior positivity (PPN, n=16), and persistent positive (PPP, n=13). After detection-based filtering, 186 putative and 64 quantitatively estimated metabolites were retained for integrated univariate, multivariate, network, pathway, and machine learning analyses. Global class separation was weak by PERMANOVA and by five-class classification, indicating that the vaginal metabolome does not reorganize broadly across all HPV states. In contrast, trajectory-specific signals were reproducible. The strongest pairwise contrast was NNP versus PPP (best cross-validated ROC AUC 0.778; permutation p=0.039). Glycolic acid was the dominant single metabolite, particularly for NNP versus PPP (Mann-Whitney p=6.96x10^-4, FDR=0.0446, AUROC=0.902; detection 88.9% versus 15.4%; combined abundance+detection FDR=0.0010). Persistent positivity was characterized by a focused uracil-high, methyl-donor/redox-low signature, including lower glycolic acid, S-adenosylmethionine, NAD+, and betaine, together with higher uracil. Ratio mining further sharpened discrimination, with uracil/S-adenosylmethionine and uracil/creatinine among the best PPP classifiers, and glucose 1-phosphate/isovaleric acid-valeric acid strongly separating NNP from NPP. These data support a model in which HPV trajectory is encoded by targeted metabolic states rather than a diffuse HPV-positive versus HPV-negative metabolomic shift.

Citrate is a central intermediate metabolite linking the tricarboxylic acid cycle and lipid biosynthesis. Tools for monitoring of spatiotemporal citrate dynamics are critical for getting a better understanding of cellular metabolism. Here, we develope genetically encoded excitation ratiometric biosensors for citrate, based on our previous intensiometric green fluorescence protein-based citrate biosensor, Citron1. We find that a single mutation in the Citron1 chromophore-forming tripeptide provided an excitation ratiometric response. Further rounds of directed evolution yield highly responsive variants, exhibiting citrate-dependent fluorescence changes between two excitation peaks. When expressed in mammalian cells, these biosensors enable citrate dynamics to be monitored in both the cytosol and mitochondria. Comparative analysis across multiple human breast cancer cell lines uncovers cell line-specific differences in citrate levels and their heterogeneity, which could be linked to their malignancy. Furthermore, flow cytometry-based measurements in mouse embryonic stem cells demonstrate the proteomics signatures underlying the population-level variability in citrate concentrations and citrate rewiring during stem cell differentiation. Together, these results show that these excitation ratiometric citrate biosensors enable quantitative, compartment-resolved, and population-scale analysis of cellular metabolism.

Symbioses are widespread (1) and underpin the function of diverse ecosystems (2-6), but their evolutionary stability is challenging to explain (7,8). Fitness trade-offs between contrasting intracellular and extracellular niches could act to stabilise endosymbioses because adaptation to either niche is predicted to reduce fitness in the alternate niche, thus reinforcing symbiosis (8,9). Here, we experimentally evolved four diverse Chlorella green algal endosymbionts of Paramecium bursaria to free-living conditions supplying either an amino acid, as provisioned by hosts (10,11), or nitrate, as available in freshwater (12), as the sole nitrogen source. Experimental algal populations adapted to free-living environments, generally increasing in population density and cellular chlorophyll content over time. In one of the four endosymbiont strains, adaptation to the nitrate free-living environment, but not the amino acid environments, drove the loss of fitness benefits to the host in reconstituted symbioses. This loss was not associated with reduced ability to grow on host-provisioned amino acids, nor lost ability to release the sugars provisioned to the host (10,13). Genome sequencing of evolved algal lines revealed genomic divergence between nitrate-adapted and amino acid-adapted lines, affecting genes involved with metabolic organisation and intracellular resource transport. Untargeted metabolomic profiling further showed extensive changes to membrane remodelling and turnover in N-evolved lines. Together, our data support a role for metabolic trade-offs driving divergence between contrasting intracellular and extracellular niches, with nitrogen as a key environmental axis driving divergence. Fitness trade-offs may, therefore, be a general, simple mechanism acting to reinforce symbiosis, contributing to evolutionary stability.

Chronic periapical periodontitis (CAP), highly prevalent worldwide, has long been regarded as non-specific inflammation. Lipophilic Cutibacerium acnes (CA) persistence in host macrophages has emerged as the pathologic background of sarcoidosis and acne vulgaris. Here we report that intracellular persistence of CA in TREM2-macrophages plays a pathologic role in CAP. We observed persistent CA in macrophages in most CAP samples. Our CA clinical isolates persist in the cytosolic space of macrophages, retarding phagolysosomal degradation accompanied by NLRP3-dependent inflammatory response. Subcutaneous injection of those isolates in vivo recapitulates subcutaneous aggregation of CA-laden macrophages. By single cell RNA sequencing analysis of defined CAP samples, we found that CA in TREM2-macrophages drives exuberant lipid droplets formation, indicating that immune cells are potential lipid provider in CAP. Our observations elucidate the mechanistic link whereby TREM2-macrophages and altered lipid metabolism provide a lipid-rich niche for CA, contributing to the pathophysiology of CAP.

Breast cancer is globally the most common cancer among women. Although the five-year survival rate exceeds 80% for patients with localized disease, it drops to approximately 30% once metastasis occurs, underscoring the urgent need to define mechanisms that drive metastatic progression. Breast is a highly innervated organ and most of its innervation is sensory. However, whether sensory neurons can directly impact breast cancer cells remains an understudied topic. Here, we show that mammary tumors have increased CGRP sensory innervation. Using our novel microfluidic Device for Cancer cell-Axon Interaction Testing (DACIT), we demonstrate that the presence of axons strongly inhibits ECM-degrading ability of cancer cells. The sensory neuron secretome suppresses assembly and function of invadopodia, which are cancer cell protrusions controlling ECM degradation, and essential for intravasation and metastasis. We identify calcitonin gene-related peptide (CGRP) as the key component of the sensory neuron secretome responsible for the inhibitory effect. CGRP signaling occurs through the CRLR/RAMP1 receptor complex expressed by breast cancer cells, inducing a rapid increase in intracellular cAMP levels in breast cancer cells, followed by an increase in RhoC activity and suppression of invadopodia and ECM degradation. Loss of RAMP1 function enhances 3D spheroid invasion, cancer cell motility in vivo and significantly increases the number and the size of lung metastatic foci. Consistently, in silico analyses of both mouse and human RNASeq data point to a link between increasingly invasive subtypes with a gradual decrease in expression of RAMP1 and CRLR. To validate in silico findings, we compare RAMP1 expression in the patient breast tumors with adjacent normal tissues, confirming the invasive breast tumors have reduced levels of RAMP1. Together, our findings identify a protective role for the paracrine CGRP signaling in limiting breast cancer invasion and metastasis. We also demonstrate how cancer cells circumvent CGRP inhibition by suppressing RAMP1 expression, highlighting CGRP-RAMP1-cAMP axis as a potential therapeutic target in breast cancer.

Upon infection, arteriviruses, coronaviruses, and other nidoviruses transform endoplasmic reticulum membranes into viral replication organelles. These include large numbers of double-membrane vesicles (DMVs) whose interior is considered the primary site of viral RNA synthesis. Early studies characterized nidovirus DMVs as sealed compartments, leaving it unclear how newly synthesized viral RNA could be exported to the cytosol. The discovery of DMV-spanning pore complexes in coronavirus-infected cells provided a plausible solution for this topological challenge. However, their structural organization, functional features, and evolutionary conservation across the nidovirus order, have remained unclear. Here, we investigated the macromolecular architecture of DMVs induced by two prototypic arteriviruses using cellular cryo-electron tomography. Despite the substantial evolutionary distance separating arteriviruses and coronaviruses, we observed DMV-spanning pore complexes with striking structural similarities to those previously described in coronaviruses. These pores appear to facilitate both export and encapsidation of viral RNA. In the absence of viral RNA synthesis, ectopic expression of the arterivirus transmembrane nonstructural proteins nsp2 and nsp3 sufficed to induce the formation of pore-containing DMVs. Together, our findings reveal the conservation of key structural features of DMV pores across two distantly related nidovirus families and support a central role for these pores in nidovirus replication.

Early behavioral and temperamental differences are important indicators of later socioemotional development and psychopathology risk, yet their neural bases near birth remain incompletely understood. Using resting-state fMRI data from the Developing Human Connectome Project, we examined whether neonatal functional connectivity predicts 18-month behavioral and temperament outcomes in 397 infants (277 term-born, 120 preterm-born). Outcomes were assessed using the Child Behavior Checklist (CBCL) and the Early Childhood Behavior Questionnaire (ECBQ). We applied a stability-driven, ROI-constrained connectome-based predictive modeling framework to identify robust whole-brain connectivity features associated with later externalizing, internalizing, surgency, negative affect, and effortful control. Significant predictive models were observed for multiple outcomes across the whole cohort as well as within term-born and preterm-born groups, with clear differences in predictive architecture between cohorts. Across analyses, prefrontal and temporoparietal systems were repeatedly implicated, alongside medial temporal, fusiform, parahippocampal, and orbitofrontal-related regions. These findings indicate that large-scale neonatal functional organization is meaningfully related to later socioemotional and behavioral variation, and that preterm birth is associated with partly distinct predictive connectivity patterns.

Childhood obesity remains a pressing global health challenge, yet the impact of dynamic adiposity changes during active developmental window retains poorly understood. Leveraging longitudinal data from the Adolescent Brain Cognitive Development (ABCD) Study (N=8519 at baseline; N=1873 at 4-year follow-up), our study reveals distinct neurodevelopmental implications of central fat dynamics during adolescence. At baseline, central fat indices (body roundness index, BRI / waist-to-height ratio, WHtR) outperformed BMI in predicting cognitive deficits, showing robust associations with impaired inhibitory control and episodic memory. The prediction effect was partially mediated by cortical changes in prefrontal and temporal regions. Longitudinally, the rate of fat accumulation ({Delta}) emerged as a critical predictor: faster adiposity accrual predicted attenuated cortical thinning (i.e., slower development) in parietal lobes and poorer executive function at follow-up, while baseline adiposity showed no significant effects on the follow-up brain morphology or cognitive development. Notably, subgroup analyses uncovered that obese adolescents with central fat reduction exhibited accelerated cortical thinning in posterior cingulate (change difference p=0.006-0.029) alongside rapid improvement in inhibitory control (Flanker slope difference p<0.05), whereas those with persistent adiposity showed delayed thinning in the postcentral gyrus. The study reveals that central fat (BRI/WHtR) is closely linked to neurocognitive risks, and longitudinal fat accumulation?rather than baseline adiposity?drives cortical alteration. Notably, fat reduction activated adaptive neural change in obese adolescents, underscoring the importance of weigh regulation during neurodevelopment.

Audition is a fundamental sense, underlying critical human behaviors such as communication and recognition. Despite its importance, how the tuning and organization of receptive fields mature from childhood to adulthood in auditory cortex has not been directly measured. Through a gamified neuroimaging approach using functional MRI, we model population receptive field (pRF) tuning for frequency across human auditory cortex in both children and adults. In the same participants, we behaviorally quantify detection thresholds for different frequencies embedded in noise to understand how the functional development of human auditory cortex drives behavior. We find that while the tonotopic organization of pRFs is qualitatively present in early childhood, there is a protracted increase in the representation of low frequencies in tonotopic maps of primary auditory cortex. This maturation of pRF tuning appears to drive basic auditory behaviors, correlating with tone detection thresholds across participants. We also observe protracted development in secondary auditory regions, offering evidence for an anatomically-predictable tonotopic map posterior to Heschls Gyrus. These data provide a new avenue for studying the development of audition in the human brain and lay important groundwork for understanding atypical development in auditory processing disorders.

How early visual cortex (EVC) represents working memory (WM) content while continuing to process incoming sensory input remains unclear. Using fMRI with prolonged delays to isolate mnemonic activity, together with analyses of cross-decoding, low-dimensional subspace structure, and representational geometry, we examined the relationship between sensory and mnemonic orientation representations in human EVC. Cross-decoding generalized poorly between sensory and mnemonic epochs, but this did not imply unrelated codes. Rather, the two occupied separable low-dimensional subspaces while preserving representational geometry across epochs. During discrimination and estimation, sensory- and mnemonic-trained decoders yielded dissociable readouts of concurrent sensory and mnemonic information from the same EVC measurements. Mnemonic coding showed little dependence on the retinotopic radial bias that characterized sensory coding, and trial-by-trial variability in mnemonic representation predicted both discrimination choices and estimation reports. Our findings support a population-level account in which mnemonic information in EVC is re-expressed in a separable but geometrically preserved format.

Structural complexity in the rice inflorescence (panicle) is determined by the activity of indeterminate meristems, which allow sequential branching events to occur but later acquire a determinate character that precludes the initiation of new growth axes. To better understand the underlying regulatory processes, we combined a detailed time-course of panicle development with tissue-specific sampling of meristems before and after the determinacy switch, monitoring global gene expression programs and hormone accumulation. This allowed the delineation of three dynamic transcriptional modules and the inference of gene regulatory networks highlighting hormone regulatory hubs associated with the indeterminate-to-determinate meristem transition. Our data confirm the importance of known regulators of inflorescence development and identify novel actors, notably genes encoding transcription factors, that were not previously described in the regulation of flowering. The combined biochemical and transcriptomic data support a model in which cytokinin signalling is particularly active during the proliferative branching phase, during which meristem maintenance is promoted while a feedback mechanism is also triggered, ultimately leading to the acquisition of determinate meristem fate later in development. HighlightInvestigating the molecular nature of rice inflorescence meristem determinacy, we studied temporal and spatial gene expression alongside hormone accumulation, identifying novel regulatory interactions and a key role for cytokinins.

Type 2 diabetes (T2D) is a heterogeneous disease shaped by genetic pathways related to insulin resistance and beta cell dysfunction, but how this heterogeneity is reflected molecularly remains unclear. We integrated partitioned polygenic scores (pPS) with proteomic and metabolomic profiling to define molecular signatures of T2D and their clinical relevance. We analyzed UK Biobank participants with genomic, proteomic, and metabolomic data. In a disease-free training subset, we used LASSO regression to identify multi-omic signatures associated with each pPS by jointly modeling proteins and metabolites. In an independent testing set, we constructed multi-omic scores and examined their associations with clinical traits and diabetes-related outcomes. Mediation analyses were used to investigate putative causal pathways. Key findings were evaluated in the Multi-Ethnic Study of Atherosclerosis (MESA). We identified distinct multi-omic signatures that capture the molecular architecture of T2D genetic risk across physiological subtypes. Compared with genetic scores alone, multi-omic pPS showed larger effect sizes and better disease discrimination. These scores recapitulated subtype-specific physiology and were associated with T2D risk. The Beta-Cell 2 multi-omic score showed marked stratification for insulin use, which was replicated in MESA, where it also predicted future insulin use. Mediation analyses implicated lipoprotein remodeling and fatty acid metabolism in the Lipodystrophy 1 cluster, accounting for up to 45% of the total effect of pPS on T2D risk. Integrating process-specific genetic risk with circulating multi-omic profiles reveals biologically distinct endotypes of T2D and supports a framework for improved patient stratification and risk assessment.

Novel (nua) Kinase 1 (NUAK1) encodes a serine-threonine protein kinase, mutations in which are associated with autism spectrum disorder. Direct phosphorylation targets of NUAK1 have been elusive hindering mechanistic understanding of its role in brain development. Here, we characterize autism-associated NUAK1 variants and show their differential impact on catalytic activity and subcellular distribution. We engineered ATP-analog sensitive NUAK1 and utilized its specificity towards bulky analogs to identify over 30 hitherto unknown direct phosphorylation targets of NUAK1. We demonstrate that Pleckstrin Homology and Sec7-domain containing protein 3 (PSD3) is a bona fide phosphorylation target of NUAK1. A guanine exchange factor (GEF) for ARF6 GTPase, PSD3 is phosphorylated by NUAK1 at S476. Expression of phosphodeficient PSD3 leads to aberrant activation of ARF6 and generation of PI(4,5)P2 that accumulates in intracellular vesicles. In neurons, phosphomutant PSD3 leads to enhanced spine maturation in an ARF6 dependent fashion. This study reveals direct neuronal substrates of an autism risk gene NUAK1, and delineates a mechanism by which PSD3 phosphorylation regulates ARF6 activation and spine maturation.

Multisensory perception is a cornerstone paradigm for understanding how the brain constructs coherent representations of the world from noisy, fragmented sensory inputs. For decades, researchers have used the magnitude of crossmodal illusions, the width of the temporal binding window, and related behavioral indices as direct proxies for integration strength, and have leveraged these measures to compare multisensory function across developmental, clinical, and aging populations. Here we argue that this descriptive practice is fundamentally compromised: behavioral readouts of multisensory integration are composite measures jointly shaped by unisensory precision, amodal priors, and the binding process itself, and cannot be interpreted in isolation. Drawing on simulations within a Bayesian Causal Inference framework, we show how identical behavioral patterns can arise from very different underlying causes, leading to systematic misattribution of group differences to deficits or enhancements in integration. We review complementary computational frameworks, including drift diffusion, multisensory correlation detection, and statistical facilitation models, and outline their respective explanatory limits. Finally, we provide a model-based inference pipeline, from experimental design and unisensory baselines to parameter estimation and interpretation, that disentangles sensory fidelity, prior expectations, and integrative tendency. Adopting this normative approach is essential for cumulative progress in basic multisensory research and for its translation to neuropsychiatric assessment, lifespan research, and artificial perceptual systems.

Certain regulatory DNA regions remain accessible even under conditions of widespread chromatin compaction. These regions are often marked by specific protein factors and histone modifications that help maintain their accessibility. Here, we examine the genomic landscape of acetyl-methyllysine (Kacme), a recently discovered histone post-translational modification. Across multiple systems, Kacme is highly enriched at sites of accessible chromatin, including active promoters, enhancers, silencers, and CTCF-binding sites. We find that Kacme is selectively retained at loci that resist condensation during mitosis, marks XIST and escapee regions on the inactive X chromosome in female cells and demarcates the boundaries of broad heterochromatin domains. Kacme-marked insulator elements block heterochromatin spreading and protect adjacent genes from transcriptional repression, even when H3K27me3 levels are pharmacologically elevated through KDM6A/6B inhibition. Taken together, our findings establish the chromatin features associated with Kacme and support a model in which Kacme helps safeguard chromatin accessibility at loci that resist compaction.